Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC1A

Cell type

Cell type Class
Neural
Cell type
hTERT RPE-1
Primary Tissue
Eye
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

source_name
RPE1 hTERT c-Myc ER
cell type
RPE1 hTERT c-Myc ER
treatment
4OH-Tamoxifen induced
timepoint
48h
chip antibody
Smc1 (Bethyl laboratories A300-055A rabbit)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The samples were washed twice in PBS and resuspended in cold ChIP buffer (25 mM Tris/HCl pH 8, 2 mM EDTA, 150 mM NaCl, 1% Triton, 0.1% SDS) plus protease inhibitor cocktail (Sigma P8340). The chromatin was sheared with a Bioruptor for 30”on/30”off for 30 minutes using Diagenode tubes. The DNA library for sequencing was prepared using 2 ng of ChIP'ed DNA for the Kapa Hyper Prep kit according to the manufacturer instructions. QC was performed using the ThermoFisher Qubit and either the Agilent BioAnalyser or TapeStation. The DNA samples were normalised and prepared into Illumina compatible libraries using the KAPA HyperPrep kit according to the manufacturer's instructions. The libraries were pooled to 4 nM and sequencing was performed on the HiSeq 4000 with at least 75bp reads.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
47798765
Reads aligned (%)
86.8
Duplicates removed (%)
9.1
Number of peaks
32783 (qval < 1E-05)

hg19

Number of total reads
47798765
Reads aligned (%)
86.1
Duplicates removed (%)
10.4
Number of peaks
32493 (qval < 1E-05)

Base call quality data from DBCLS SRA